In a large saute pan over medium-high heat, add ground beef and half of taco seasoning. Cook and crumble until you no longer see pink and meat is cooked through.
In a saucepan over medium heat, add refried beans, one cup of cheddar cheese and remaining taco seasoning. Stir together until cheese is melted.
Preheat oven to 425degF.
To build one pizza - spread half of bean mixture on parcooked pizza dough. Sprinkle with half of cooked beef and one cup of cheese. Repeat with second pizza. Place in oven to bake for 12 minutes.
In a small bowl, combine onion, jalapeno, cilantro, lime juice and salt. Toss to coat and set aside.
Remove from oven and sprinkle each pizza with half of onion mixture and half of remaining cheese. Last layer up with tomato slices.